The genome of Arabidopsis thaliana consists of 10 chromosomes. By inducing CRISPR-Cas–mediated breaks at subcentromeric and subtelomeric sequences, we fused entire chromosome arms, obtaining two eight...

Abstract. A lack of recombination in the heterogametic sex between parts or all of newly evolving sex chromosomes results in the gradual accumulation of de

Certain genes, chromosomes, organelles, or entire sets of chromosomes can bias their transmission to the next generation, propagating themselves at the expense of the rest of the genome. Referred to …

Background Whole-genome sequencing efforts, have during the past decade, unveiled the central role of genomic rearrangements—such as chromosomal inversions—in evolutionary processes, including local a...

A combination of whole-genome NanoSeq with deep whole-exome and targeted NanoSeq is used to accurately characterize mutation rates and genes under positive selection in sperm cells.

Background Whole-genome sequencing efforts, have during the past decade, unveiled the central role of genomic rearrangements—such as chromosomal inversions—in evolutionary processes, including local a...

Telomeres are essential for maintaining genomic integrity and are associated with cellular aging and disease, yet the factors influencing their inheritance across generations remain poorly understood....

Abstract. Cichlid fishes have undergone an extraordinary diversification in East Africa. They also have a high rate of sex chromosome turnover. This clade

Nature Reviews Genetics, Published online: 24 September 2025; doi:10.1038/s41576-025-00895-2Haplotype phasing and genotype imputation improve genomic analyses by determining which variants occur together on a chromosome and inferring unobserved varants, respectively. In this Review, Sun and Li describe how tools for haplotype phasing and genotype imputation have evolved to accommodate increasingly larger genomic datasets and new sequencing technologies.

Sexual maturation is a key developmental process important for reproductive success. Understanding the molecular mechanisms behind variation in sexual maturation can provide insights into reproductive biology and how life history variation is encoded in the genome. Atlantic salmon (Salmo salar) has become an excellent sexual maturation research model due to its diversity of life history strategies and its ecological and economic importance. A major challenge has been the lack of a comprehensive transcriptional investigation of reproductive tissues that captures the dynamic transcriptional changes across individuals, tissues, and developmental stages. Long non-coding RNAs (lncRNAs) also play crucial roles in maturation, yet their functions in salmon maturation remain underexplored. In this study, we sequenced 98 transcriptomes and found substantial transcriptomic complexity in the gonad and pituitary tissues of Atlantic salmon. We identified transcripts corresponding to 2,364 putative newly characterized protein-coding genes and 4,421 putative long intergenic non-coding RNAs (lincRNAs), many with tissue-specific expression. Gene co-expression network analysis (WGCNA) revealed tissue-specific gene network modules, linked to GO terms including Wnt signaling in immature testis, lipid metabolism, and cilia assembly in mature testis, ribosome biogenesis and DNA repair in the ovary, and hormone activity in pituitary. We identified new copies of known genes, such as gh1, pou3f2, and ier5 associated with the regulation of gonadal and pituitary functions. Some lncRNAs and their nearest genes showed correlated expression within modules, suggesting potential regulatory roles. Candidate lincRNAs indicated cis-acting regulatory potential on genes like tnfrsf11b and fgl1, which are implicated in immune privilege during gonadal development and sperm quality control. Our study provides a comprehensive transcriptomic analysis of Atlantic salmon gonad and pituitary tissues, significantly improving the functional annotation of the Atlantic salmon genome. These findings reveal key regulatory pathways and novel molecular players involved in sexual maturation, particularly in the testis. Importantly, our study highlights the regulatory potential of lncRNAs in reproductive biology and maturation age variation, advancing our understanding of the molecular mechanisms governing sexual maturation. They further unlock future gene expression analyses and regulatory network reconstruction for dissecting the roles of lncRNAs in Atlantic salmon life history variation.

In the past three decades, fish abundance, richness and uniqueness have diverged across cold and warm streams, and the effects on native fish communities of stream warming and increases in introduced fishes have magnified each other.

Abstract. The first influential hypothesis for sex chromosome evolution was proposed in 1914 by H. J. Muller, who argued that once recombination was suppre

Chromosomal inversions are ubiquitous across the Tree of Life, with genome-wide studies revealing a bias toward smaller inversions, yet research has disproportionately focused on large, supergene-like...